Best Protest Signs. Ever.

If God designed us the way we are, can I sue Him for my scoliosis?

Awesome opinion piece. I had dreamed of getting 100 people to show up wearing fake green beards to these kinds of events, but that would have been too esoteric.

I am simply amazed at the gall of these people trying to keep flyers from being distributed by hand. They ought to lodge a formal protest with the university against the sponsoring organization. The DI ought to get banned for behaving like that.

Interesting to hear Behe and the others finally becoming a bit more honest for a change. Too bad we don't know the name of the ID Prop. who admitted that the DI's mission was true.

By a coincidence (or "coincidence"), SMU is also going to be the site of the George W. Bush presidential library. Seriously.

I'm quoting from memory, but if I recall correctly, there are already protests that some kind of monstrous structure is going to disrupt the "graceful Georgian campus located in a well-to-do suburb".

I'm not sure that the futurologists at SMU are doing a great job of forecasting. Maybe the Methodists at SMU should have asked the Baptists at Baylor for some advice about ID.

If God designed us the way we are, can I sue Him for my scoliosis?

By a coincidence (or "coincidence"), SMU is also going to be the site of the George W. Bush presidential library.

I live in Seattle. Who wants to join me with some signs near the corner of 3rd & Pike?

The mammalian mitochondrial ribosome (mitoribosome)1 has a smaller sedimentation coefficient (55 S), compared with the bacterial ribosome (70 S), and consists of large 39 S and small 28 S subunits (5). The former contains 16 S and the latter contains 12 S rRNAs as RNA components. The mammalian mitoribosome contains no counterpart for the 5 S rRNA found in bacteria. A recent physicochemical study has revealed that the rat mitoribosome has a large molecular mass (3.57 MDa) compared with that of the Escherichia coli ribosome (2.49 MDa) (6), which is explained by the fact that the protein to RNA ratio is completely reversed between these two ribosomes (7). The protein composition of the mitoribosome has been estimated to be about 75%, which indicates that large parts of bacterial rRNA domains have been replaced by protein components during mitochondrial evolution from a eubacteria-like endosymbiont in eukaryotic cell progenitors.

Wow! Is this THE Paul Nelson of "ontogenetic depth" fame who PZ says is 3 years tardy with an answer to his question?

Perhaps, Paul, you could answer this question:

What would the "ontogenetic depth" be of a radio falling from an average sized apartment building onto

a) concrete
b) loose beach sand
c) a plate of cheese nachos

I await your reply.

p.s. If you are not THE Paul Nelson then forget the above and carry on. That is all.

Maybe it's my tiny brain, but my wisdom teeth haven't caused me any trouble. (I know they are a bitch to keep clean, but the primary reason to pull them hasn't surfaced). Not sure if I got an evolutionary advantage or what.

Immediately, the only person on stage with any knowledge of biology, Michael Behe, took up the question. His answer was that ID theory does not allow for explanations regarding interspecies commonalities such as those implied in the question.

Immediately, the only person on stage with any knowledge of biology, Michael Behe, took up the question. His answer was that ID theory does not allow for explanations regarding interspecies commonalities such as those implied in the question. In short, his answer was that he couldn't explain it with ID theory.

"By a coincidence (or "coincidence"), SMU is also going to be the site of the George W. Bush presidential library. Seriously."

I think the word is

co-inky-dink.

Comment #170746 Posted by Sir_Toejam on April 18, 2007 8:05 PM (e) | kill If God designed us the way we are, can I sue Him for my scoliosis?

RSR also implicitly raises the ancient mystery "If humans evolved from other primates, why are there still creationists"?

"Why do the ribosomes (protein synthesizing machinery) in our mitochondria match those of bacteria?" They do?

The mammalian mitochondrial ribosome (mitoribosome)1 has a smaller sedimentation coefficient (55 S), compared with the bacterial ribosome (70 S), and consists of large 39 S and small 28 S subunits (5). The former contains 16 S and the latter contains 12 S rRNAs as RNA components. The mammalian mitoribosome contains no counterpart for the 5 S rRNA found in bacteria. A recent physicochemical study has revealed that the rat mitoribosome has a large molecular mass (3.57 MDa) compared with that of the Escherichia coli ribosome (2.49 MDa) (6), which is explained by the fact that the protein to RNA ratio is completely reversed between these two ribosomes (7). The protein composition of the mitoribosome has been estimated to be about 75%, which indicates that large parts of bacterial rRNA domains have been replaced by protein components during mitochondrial evolution from a eubacteria-like endosymbiont in eukaryotic cell progenitors.

See T. Suzuki et al., "Proteomic Analysis of the Mammalian Mitochondrial Ribosome," Jl Biological Chem 276 (2001):33181-33195.

Dr. Nelson,

Would you be so kind as to explain your reference's figures four and five and the patterns found therein, without utilizing common descent? As a personal request, would you be so good as to explain them using Intelligent Design? I first heard of ID around about 1999, and I know it has been around for nearly 20 years now, but I've never heard it used to explain this kind of data. I'd also like an explanation for the following: "Among the 21 proteins in the small subunit, 13 proteins were identified as prokaryotic homologues and eight proteins were specific to the mammalian mitoribosome (Table I). The amino acid sequences of the human and mouse mitoribosomal proteins along with their counterparts from other animal mitochondria and prokaryotes were aligned as shown in Fig. 4. Significant homology between mitoribosomal proteins and their bacterial counterparts indicates that the distribution of proteins within the mitoribosome and the prokaryotic ribosome is similar, as observed in a previous study on 39 S large subunit proteins (22)." How about explaining ref 22? You had some reason for picking out this paper so I'm sure you're quite knowledgeable about its contents so this should be no problem for you.

You did read it, right?

a library of comic books?

don't forget the beer bong and several available mirrors and handy one-sided razor blades.

can't enjoy the library without refreshments, after all.

Dr. Nelson, Would you be so kind as to explain your reference's figures four and five and the patterns found therein, without utilizing common descent sense? As a personal request, would you be so good as to explain them using Intelligent Design?

— DMA

"Why do the ribosomes (protein synthesizing machinery) in our mitochondria match those of bacteria?" They do?

— Paul Nelson

Just enough data to confuse the faithful while ignoring the rest. I see a hint of young earth creationism shining through. Sal, oh Sal where are you.

BLAST it:

[Behe's] answer was that ID theory does not allow for explanations regarding interspecies commonalities such as those implied in the question.

To Mr. Kellogg: You have scoliosis because of original sin. When you are raptured up to heaven at the end of times if you are a true believer your spine will be perfect. Any questions/-please consult your nearest premillenial dispensationalist..Your presence at this website; however, may bring your religious sincerity into question.

I'm liking my creo theory more and more. They have decided to suspend disbelief permanently and enter into a fantasy world. We all do this when watching a movie, TV, or reading a fiction book, temporarily.

The protein composition of the mitoribosome has been estimated to be about 75%, which indicates that large parts of bacterial rRNA domains have been replaced by protein components during mitochondrial evolution from a eubacteria-like endosymbiont in eukaryotic cell progenitors.

Behe actually answered the question initially appropriately, saying that the current scientific understanding is that mitochnodria were mostly likely independent prokaryotic organisms that were symbiotically appropriated by eukaryotic ancestors.

Once granting this scientific explanation, Behe then claimed that science cannot explain how or why this symbiotic relationship was formed. His reference to radios falling into cars was his way of illustrating how unlikely it would have been for this relationship to form by random chance. The implication, of course, was that since science supposedly cannot explain it, and it was too unlikely to happen by chance, therefore the Designer must have taken the two organisms and placed them together, creating eukaryotic life.

pro from dover:

Scoliosis from his original sin... but what do you have from yours?

Does the human intellect come from original sin as well? The ability to question the dogma fed to us from toddlerhood onward certainly sounds like a punishment Yahweh/Allah/Vishnu/Zeus/Odin/Zoroaster would have given us.

"Behe then claimed that science cannot explain how or why this symbiotic relationship was formed. His reference to radios falling into cars was his way of illustrating how unlikely it would have been for this relationship to form by random chance."

Really. So I guess the fact that there are some species of amoeba that have aerobic bacterial endodymbionts doesn't count as "understanding". Come on, this is not just something that happened a billion years ago. We can still observe this process going on and can duplicate it in the laboratory.

The "how" is engulfment by endocytosis. The "why" is mutualism. The endosymbiont benefits by getting a protected place to live and access to nutrients. The host gets an efficient mechanism of arerobic respiration and a source of ATP. That is why the relationship has been so stable and profitable.

Of course how or why are not nearly as important as the fact that it actually did occur. The genetic evidence is quite clear that it did, which Behe does not seem to dispute. Given that, how unlikely it would have been becomes irrelavent.

"Maybe it's my tiny brain, but my wisdom teeth haven't caused me any trouble. (I know they are a bitch to keep clean, but the primary reason to pull them hasn't surfaced). Not sure if I got an evolutionary advantage or what."

If you can't keep them clean, then they will definitely cause you problems eventually. I suggest pulling them one every 6 months or so. You get REALLY good drugs! I wish I had a few more to get pulled.

The Pro's price for Original Sin must be a minor form of Cassandra's curse if anyone is taking his last comment literally. Longtime readers know him for what he is.

David Stanton -

Although I strongly agree with you that the evolution of eukaryotic cells is a viable topic for science (and vehemently disagree with Behe's hypocritical and politically motivated claim that it isn't), unless I'm misunderstanding something, amoebae with symbiotic bacteria are a partial analogy at best.

This is because amoebae are already eukaryotes. They already have eukaryotic ribosomes, mitochondria, a nucleus, and so on. What we don't see in the present, to the best of my knowledge, is any cellular life that has traits intermediate between eukaryotes and prokaryotes.

Paul Nelson -

Funny, I was going to point out the minor differences between eukaryotic and prokaryotic ribosomes for clarity.

Maybe if you actually read some real science carefully and objectively, you might enlighten yourself a little.

"Why do we have wisdom teeth if they do not fit our jaws?"

You could be a mutant- (think Jeff Foxworthy's "You could be a redneck")

If your jaw is too small to accomodate all of your teeth, you could be a mutant.

Also, pertaining to endosymbiosis:

" Many researchers think eukaryotes are the descendants of either bacteria or archaea, or some combination of the two. But genetic and protein evidence do not support this view, researchers report in Friday's issue of the journal Science, published by AAAS, the nonprofit science society."

"Instead, the data suggest that eukaryote cells with all their bells and whistles are probably as ancient as bacteria and archaea, and may have even appeared first, with bacteria and archaea appearing later as stripped-down versions of eukaryotes, according to David Penny, a molecular biologist at Massey University in New Zealand."

See Can evolution make things less complicated?

For at least 12 years Behe is on record admitting that "interspecies commonalities" are transmitted through "biological continuity," his most recent rephrasing of the politically incorrect "common descent". So, technically, ID has no need to explain them because it is not challenging mainstream science (evolution) with respect to that particular question.

Too bad we don't know the name of the ID Prop. who admitted that the DI's mission was true.

"I wonder which of the four said it." It was Stephen Meyer, actually. I've got the exchange virtually transcribed in my notes, and I'll be posting a lot of the question-and-answer session on my blog later.

Can genetic similarities also be explained by convergence? If "yes" that alone can explain the similarities observed in ribosomes.

Also is there any way to objectively test the premise that free-living bacteria can engulf another free-living bacteria and in the end wind up a eukaryote?

Technically (for the few IDists who agree with Behe, that is), sure.

"By a coincidence (or "coincidence"), SMU is also going to be the site of the George W. Bush presidential library. Seriously."

To be fair, hosting a presidential library does not imply agreement with the administrations policies. This library could be a gold mine for historians for generations to come. The list of controversies in this administration is endless.

Since Bush is a Texan and a Methodist, it is quite reasonable for him to donate his papers to the largest Methodist university in Texas.

Regards,
Jim

JoeG -

Those are good questions.

It would be fascinating if some or all bacteria were descended from early eukaryote mitochondria, not the other way around.

I suppose that this would be vaguely analogous to the evolution of viruses, which are thought to have descended from cells. (Since viruses require intact cells for replication, it is much less controversial that cells most likely came first.)

Of course, if eukaryotes came before prokaryotes, that raises the big question of where eukaryotic cells came from. Note that this would not in any way weaken the theory of evolution, which applies to cellular and post-cellular life. Nor would it make "eukaryotic cells are complex so they must have been poofed into existence by magic" a valid scientific answer. (Although I'm a non-atheist who firmly believes that the origin of life is a natural, scientific question, it is theoretically possible, if strained, for someone to argue that a supernatural entity magically created the first life of earth, and evolution took over after that, without running afoul of definitive current science.)

The symbiosis argument is obviously still plausible. For one thing, if mitochondria were organelles first and independent bacteria second, how did they come to have their own DNA? (Of course, we can think of hypothetical answers to this, but it is a tough question).

As for whether survivors of consumption by predators can be ancestors to symbiotes with the predators, I can't provide an example, but it sounds plausible, and I bet someone else will.

The protein composition of the mitoribosome has been estimated to be about 75%, which indicates that large parts of bacterial rRNA domains have been replaced by protein components during mitochondrial evolution from a eubacteria-like endosymbiont in eukaryotic cell progenitors.

To be fair, hosting a presidential library does not imply agreement with the administrations policies.

As I read Paul Nelson's comments, I find it impossible to believe that he is not dissembling on purpose. His answers contain enough "jargon" to sound superficially plausible, but he avoids basic questions asked in a straightforward manner. To recap:

1. The protesters held up signs indicating the similarity between ribosomes in human mitochondria and bacteria;

2. Nelson confidently stated that they do not, in post #170755, ostensibly supported by a citation to a paper from Suzuki;

3. Numerous posters pointed out that (a) the evidence, including Suzuki's paper, supports the original claim and not Nelson's, and (b) that the Suzuki paper flatly contradicts ID;

4. Nelson responds, in post #170895, but does not address point (a) at ALL, and responds to point (b) only to give an answer on the level of Dembski's "street theater" answer; "Oh, it's okay, I just posted the reference to make you think."

No, Paul, you didn't. You confidently asserted that human mitochondrial ribosomes are not similar to bacteria, tried to slough it off with a science-y-sounding citation, and got called on it. You're dead wrong, and your source does not support the argument you initially made.

Failing to acknowledge that, and worse, changing the subject -- those are the hallmarks of a professional charlatan.

worse, changing the subject

Andrew,

Does "uniformitarian" as a character string match "non-uniformitarian"? Well, yes, in one sense: the strings share 14 out of 17 letters, in identical positions (if one aligns them after the hyphen, and begins counting matches there). Better than 82 percent similarity.

Can one therefore substitute one word for the other in a text, without loss of meaning? No.

Evolution is not, au fond, a theory of similarity. It is a theory of transformation. Differences in two molecular complexes, or machines (the eukaryotic mitochondrial ribosome vs. bacterial ribosome) are as relevant as similarities, when assessing hypotheses about their origin and evolution. The Suzuki et al. paper gives evidence of differences between the two complexes, which must be weighed when evaluating theories about the origin of mitochondrial ribosomes.

To the airport.

Can one therefore substitute one word for the other in a text, without loss of meaning? No.

Put another way, what molecular characters would show that eukaryotic mitochondrial ribosomes and bacterial ribosomes arose independently of each other? One cannot say that similarities count as evidence for common ancestry, unless one knows what would count as evidence against common ancestry.

Evolution is not, au fond, a theory of similarity. It is a theory of transformation.

Harold,

The organism I mentioned lacks mitochondria. In that sense at least it is "intermediate" between prokaryotess and eukaryotes. That is why it is beneficial for it to have the symbiotic bacteria. I don't know for sure that it has been demonstrated that that species lacks mitochoindrial as an ancestral condition. If so, that would be even stronger evidence for the endosymbiotic theory.

It is also my understanding that these types of experiments can be repeated in the lab with two prokaryotes. I will have to try to look up some references about this, unless someone else can help me out here.

As regards convergence, the genetic similarities cannot easily be explained by convergence. The probability is simply too low. In addition, the sequence data point to a particular group of purple bacteria as ancestral to mitochondria and there is good evidence form other types of data that this is probably the right answer. The animal mitochondrial genome is so degraded compared to any bacterial genomes that the hypothesis that bacteria could have been derived from mitochondria is also ruled out, unless this occurred very soon after the symbiosis event. Still, this could not have been the origin of all bacteria, since they appear significantly before eukaryotes in the fossil record. Likewise, we also know from sequence data that there was an independent origin of chloroplasts and chloroplast DNA, undoubtedly after the mitochondrial event.

The endosymbiotic theory is well supported by several different independent data sets. It is definately the most parsiminous explanation for all the data. Pretending that we don't understand this at this point is, once gains, ignoring all the evidence.

The evidence for endosymbiosis is, IMO, quite compelling. For example, a prediction of the endosymbiotic model for the origin of mitochondria is that the inner and outer mitochondrial membranes should have different characteristics since the outer should be a remnant of the host cell and the inner should be similar to the plasma membrane of prokaryotic cells. Studies of have shown that the outer mt membrane is similar to ER (i.e., eukaryotic!) and the inner mt membrane is similar to the PM of prokaryotic cells. Furthermore, the case for an endosymbiotic origin of the chloroplast is even stronger (again, my opinion) than that for mitochondria. Chloroplasts have many of the same features that link mitochondria to the prokaryotes (circular DNA, 70S ribosomes). The evidence from numerous molecular phylogenetic markers makes a strong case for cyanobacteria as the primary endosymbiont. We even have an extant example of what an intermediate might look like. The Glaucocystophytes are algal protists that, at first glance, appear to possess chloroplasts. However, a closer examination reveals that the "chloroplasts" are actually cyanobacteria (some even with peptidoglycan cell wall material still present!) that are functioning like chloroplasts. As a consequence, these chloroplast-like structures have been termed cyanelles and are interpreted as another "experiment" in primary endosymbiosis. The evidence for secondary endosymbiosis (eukaryote + eukaryote) is also compelling. One of the best cases for secondary endosymbiosis is found in the Chlorarachniophyta. These green amoebae do indeed possess functional chloroplasts. Ultrastructural analysis of Chlorarachnion revealed a rather peculiar feature--in addition to a large central nucleus, a second, smaller nucleus is present. This smaller nucleus, now called a nucleomorph, is always associated with a chloroplast. In fact, the chloroplast (with its own double-membrane system) and the nucleomorph are surrounded by a separate membrane. The clear inference is that a heterotrophic amoeba engulfed a photoautotrophic green alga, resulting in the modern day Chlorarachniophyta. This interpretation is supported by molecular phylogenetic analysis of the various genomes present in the cells of Chlorarachnion. We also know that engulfment, without complete digestion is possible. A number of molluscs (e.g., some sea slugs) engage in kleptoplasty. As the name implies, these "animals" consume chloroplast-bearing organisms (usually algae). However, they harvest and retain the still functional chloroplasts, exploiting the capabilities of the stolen organelle. Eventually, the chloroplasts die, but the mollusc need only resume grazing in order to re-stock.

While we certainly don't have all the answers, the study of eukaryote origins, within an evolutionary framework, has been a remarkably fruitful endeavor.

Andrew, please consider the possibility that you are being hasty vs Paul Nelson. For one thing, in post #170755 he said "They do?" which is not quite how you related it. More generally, Paul is a sincere Young Earther. He see things differently than you. Try re-doing your analysis from the point of view of Morton's Demon. Should you apologize to Paul?

"Put another way, what molecular characters would show that eukaryotic mitochondrial ribosomes and bacterial ribosomes arose independently of each other? One cannot say that similarities count as evidence for common ancestry, unless one knows what would count as evidence against common ancestry."

The phylogenetic position relative to other groups based on DNA sequences is how these relationships were defined. This is how we know that mitochondria were derived from purple bacteria and chloroplasts from green bacteria such as cyanobacteria and not from a common ancestor from a single symbiosis event. If the sequences were more similar to any eukaryotic lineage, then we would not conclude a prokaryotic origin. Remember, this was not the easy answer. This theoiry had to be subjected to many different tests before it was accepted. It has already passed those tests.

hallmarks of a professional charlatan.

If similarities are evidence of common ancestry, then dissimilarities are evidence of --- what?

One cannot say that similarities count as evidence for common ancestry, unless one knows what would count as evidence against common ancestry.

Really, DI has a lot of philosophers instead of scientists

scumpond: fascinating. [Yet another sentence I never thought I would utter. :-) ]

Pete: I find the applications of sundry demons in science fascinating. However, I would think YEC:ers see it differently. Oh, wait...

philosophers rather than solopists [sic].

Beware of assuming the point at issue.

— Paul Nelson

David Stanton writes: "The organism I mentioned lacks mitochondria." Could you please specify the organism? The eukaryotes previously thought to be primitively amitochondriate have been found to have small degenerate ones after all.

The paper brought up as a news item is last year's. Penny's website . Not everyone agrees with the standard endosymbiosis hypothesis yet. One of the big problems is simply that eukaryote diversity is severely understudied as yet.

David Stanton -

That's quite interesting.

I had a vague feeling that there might be amoebae without mitochondria (should have remembered that from parasitology). However, I did a brief check and found lots of articles about amoebic mitochondria, so I disregarded the proddings of my unconscious mind.

This is a link to a very brief abstract of a relatively recent article that talks about endosymbiotic bacteria in amoebae, but not with regard to mitochondria per se.

http://www3.interscience.wiley.com/cgi-bin/abstract/109900643/ABSTRACT?CRETRY=1&SRETRY=0

On the other hand, the link below leads to the abstract of a paper that suggests that modern amoeba lineages without mitochondria may be descended from ancestors that had them. In case this link just takes you to the pubmed homepage, the reference is below.

http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&cmd=Retrieve&dopt=AbstractPlus&list_uids=11830664&query_hl=1&itool=pubmed_docsum

Proc Natl Acad Sci U S A. 2002 Feb 5;99(3):1414-9

So the evidence for endosymbiosis is strong, but there is still some room for controversy. This is an area of ongoing scientific investigation, it would seem.

Pete,

The organism I was referring to was Pelonyxa (not sure that is the correct spelling). Apparently there are many such amoeba that lack mitochondria. Thanks to Harold for the reference. If these organisms come from lineages that had mitochondria, then the question becomes - did they lose the mitocondria for some reason and then acquire endosymbionts, or did they acquire endosymbionts and then lose the mitochondria. Perhaps the reference cited will give some clue.

Paul Nelson sulked -

"Put another way, what molecular characters would show that eukaryotic mitochondrial ribosomes and bacterial ribosomes arose independently of each other? One cannot say that similarities count as evidence for common ancestry, unless one knows what would count as evidence against common ancestry."

Short Answer - As you know, anything but similarity would fail to support common ancestry of the ribosomes.

Long Answer - As you know, when Darwin first articulated what was to become the theory of evolution, the very idea that bacteria existed was still the subject of debate, and the idea that they could cause disease was intensely controversial.

The theory at that time was morphology based. Still, scientists could easily distinguish superficially similar organisms that weren't closely related and superficially different organisms that were, based on such core concepts as whether they were marsupials or placentals, or the like.

Soon, biochemistry expanded rapidly. The theory of evolution predicted similar, preserved biochemical pathways. Had different forms of life had radically different biochemical pathways, the theory might have been challenged. But great similarity was found among biochemical pathways throughout life.

Classical Mendelian genetics emerged. Again, it might have led to doubts about evolution, but instead, the evidence was confirmatory.

Molecular genetics and modern cell biology emerged. Again, it was clear what the the theory of evolution predicted. Again, it was clear that the theory of evolution could be cast into doubt if unexpected results emerged. Again, a powerful independent line of evidence not only supported, but expanded and strengthened, the theory of evolution.

In every case, of course, it was not just similarity across life that was detected, but the same pattern of relationships that were suppored. Rabbits are more related to weasels than they are to moss, no matter what metric you look at.

Others say you present a false choice. I disagree. It's obvious what would count as evidence against common ancestry.

What degree of similarity across all of life do we need to infer common descent? That's an intriguing question, which you may have meant to imply. The molecular genetic, biochemical, and cell structural commonalities across life are so overwhelming, and the degrees of relationship between lineages so obvious from so many independent lines of evidence, that the question is effectively moot except for details like trying to decide the relationship between different lineages of amoebae. Whatever the threshold is, we're so far over any reasonable threshold that it doesn't matter.

At this point, of course, the evidence of common ancestry is so powerful that in order to "overturn" it, a great deal of very strong, objective evidence (and not any amount of childish word-game playing) would be required. However, it is crystal clear that there is such a thing as evidence for common descent, that there is such a thing as evidence against common descent, and that what we see over and over again is evidence FOR common descent.

David Stanton -

That's Pelomyxa; I googled it.

http://en.wikipedia.org/wiki/Pelomyxa

The current endosymbiosis explanation would be that they evolved from an ancestor that had endosymbionts, and then lost their mitochondria later, I presume. Whereas some other amoebic lineages did not lose their mitochondria.

Obviously, if there were some amoebic lineages with a primary lack of mitochondria - never had any ancestor that had them - that would support endosymbiosis even more. But the existence of these guys doesn't argue against it.

I believe that the issue of which amoebae have mitochondria may be a bit more complex that our discussion has suggested, but I have to drag myself away from this topic.

David Stanton -

That's Pelomyxa; I googled it.

http://en.wikipedia.org/wiki/Pelomyxa

The current endosymbiosis explanation would be that they evolved from an ancestor that had endosymbionts, and then lost their mitochondria later, I presume. Whereas some other amoebic lineages did not lose their mitochondria.

Obviously, if there were some amoebic lineages with a primary lack of mitochondria - never had any ancestor that had them - that would support endosymbiosis even more. But the existence of these guys doesn't argue against it.

I believe that the issue of which amoebae have mitochondria may be a bit more complex that our discussion has suggested, but I have to drag myself away from this topic.

Paul Nelson, enough of this evilution talk, please tell us the story again where the Earth is only 6000 years old! The truth is out there and you're just the man to tell the world!

@ Sir Toejam, re books for Bush Library: Bush's Fart Joke Legacy.

"Turning to the Bush clan, we learn in Kitty Kelley's book The Family: The Real Story of the Bush Dynasty that New Yorker writer Brendan Gill was once a guest of George H.W. and Barbara Bush at their summer house in Kennebunkport, Maine. Stumbling through the place late at night in search of something to read, the only volume he could find was The Fart Book."

Wow, he and Bill Dembski share some, er, tastes.

Wow, he and Bill Dembski share some, er, tastes.

Nelson--One cannot say that similarities count as evidence for common ancestry, unless one knows what would count as evidence against common ancestry.

Saying that some REs are functional and some REs arent functional is a tautology, rendering evilution an unfalsifiable just-so story! Game over, everybody go home! LOL!

Saying that some REs are functional and some REs arent functional is a tautology...

Others say you present a false choice. I disagree. It's obvious what would count as evidence against common ancestry.

Does "uniformitarian" as a character string match "non-uniformitarian"? Well, yes, in one sense: the strings share 14 out of 17 letters, in identical positions (if one aligns them after the hyphen, and begins counting matches there). Better than 82 percent similarity. Can one therefore substitute one word for the other in a text, without loss of meaning? No.

— Paul Nelson

With arguments like this, how do the IDers get anywhere at all?

"Why do the ribosomes (protein synthesizing machinery) in our mitochondria match those of bacteria?" They do?

now you know why "whoa nelly!" doesn't spend much time here at PT

If similarities are evidence of common ancestry, then dissimilarities are evidence of --- what?

Why does Paul Nelson usually have to run off and get on a plane when questions get tricky?

Once again Harold is correct. The evidence for common ancestry in all known life forms is so overwelming that it cannot really be doubted. Therefore, since all organisms did share a common ancestor at some point in the past, similarity is indeed evidence of common ancestry (usually) and dissimilarity is (usually) evidence of more distant relationships.

As to what would constitute evidence of independent origins, one could speculate. For example, if life was found on another planet, how could we tell that it was not a contaminant from earth but truly alien. Here are some speculative possibilities:

(1) Not cellular
(2) Not DNA based
(3) Drastically different genetic code
(4) "Multicellular" forms without organelles
(5) "Enzymes" not usually made of proteins

While none of these things might be absolutely conclusive by itself, a combination of them would certainly be difficult to reconcile with a common origin shared with life on earth.

And by the way, BC is also correct. If the organisms were based on the same structures and mechanisms found on earth and they shared the same genetic "mistakes" and "errors" shared by earth organisms, it would be extremely difficult, if not impossible, to argue for a comon origin.

Why does Paul Nelson usually have to run off and get on a plane when questions get tricky?

Put another way, what molecular characters would show that eukaryotic mitochondrial ribosomes and bacterial ribosomes arose independently of each other? One cannot say that similarities count as evidence for common ancestry, unless one knows what would count as evidence against common ancestry.

Hmm... if one were to show that the catalytic core of the eukaryotic ribosomal peptide synthase was fundamentally different from that of the bacterial ribosomal peptide synthase (such as not consisting of an RNA), one would pretty clearly conclude that they do not share a common ancestry.

The evidence for common ancestry in all known life forms is so overwelming that it cannot really be doubted.

The meaning, role in biology, and support in evidence of the universal "Tree of Life" (TOL) are currently in dispute (1---15). Some evolutionists believe (i) that a single rooted and dichotomously branching representation of the relationships between all life forms is appropriate (at all levels above species), because it best represents their history; (ii) that we can with available data and methods reconstruct this tree quite accurately; and (iii) that we have in fact done so, at least for the major groups of organisms. Other evolutionists question the second and third of these beliefs, holding that data are as yet insufficiently numerous and phylogenetic models as yet insufficiently accurate to allow reconstruction of life's earliest divisions, although they do not doubt that some rooted and dichotomously branching tree can in principle represent the history of all life. Still other evolutionists, ourselves included, question even this most fundamental belief, that there is a single true tree. All sides express confidence in their positions, and the debate often seems to be at an impasse (see for instance refs. 9---12).

Ask yourself why --- if their catalytic cores were different --- one would infer separate ancestry. Answer: the [biochemical] differences would be too great to allow preservation of function during the transformation of structure from a common ancestor. That is, the differences would violate what Francis Crick and Leslie Orgel called the Principle of Continuity: the only absolutely necessary condition for any evolutionary transformation is that essential function not be lost. No postulated evolutionary transformation can violate the Principle of Continuity. Observed (real) differences between eukaryotic mitochondrial ribosomes and bacterial ribosomes do not count, for Art and others, as evidence sufficient to trigger the Principle of Continuity. That means they must know the Principle of Continuity has been satisfied: the changes required to transform the common ancestral ribosome into the different systems we see today are known to be biologically possible.

"Still other evolutionists, ourselves included, question even this most fundamental belief, that there is a single true tree."

Paul,

Thanks for the reference. I guess these guys have the answer to your question about what would count as evidence against common ancestry.

Mike Syvanen and others have written here at PT about the increasingly lively debate now ongoing within evolutionary theory about the early history of life. The universal Tree, or universal common descent, has become a locus of controversy. Some investigators, such as Carl Woese and W. Ford Doolittle, strongly reject a single Tree

Because I travel too much.

While you're here, Dr. Nelson, there is a question that I've been wondering about for some time. This isn't intended as a "gotcha" question--- it's something that I really don't know the answer to. Living organisms show a very strong pattern of hierarchically nested traits. I've heard the argument that "a common designer leads to common design", but this doesn't account for a hierarchically nested pattern. I've never heard any ID proponent try to explain that pattern in terms of design. In fact, I've never heard of any plausible explanation for that pattern other than common descent with modification. Do ID proponents have an explanation for this pattern? If so, what is it?

He [Nelson] further stated that evolutionary theory today has much greater explaining power than ID and that ID consequently should not be taught in schools.

Principle of Continuity: the only absolutely necessary condition for any evolutionary transformation is that essential function not be lost.

Answer: the [biochemical] differences would be too great to allow preservation of function during the transformation of structure from a common ancestor. That is, the differences would violate what Francis Crick and Leslie Orgel called the Principle of Continuity: the only absolutely necessary condition for any evolutionary transformation is that essential function not be lost. No postulated evolutionary transformation can violate the Principle of Continuity.

I don't know what Crick claimed, however it is believed that in many cases essential function is lost when genes are duplicated. This frees up genetic material to effect some other function.

Nelson cites: W.F. Doolittle and E. Baptest(s)e, "Pattern pluralism and the Tree of Life hypothesis," PNAS 104 (February 13, 2007):2043-2049. The meaning, role in biology, and support in evidence of the universal "Tree of Life" (TOL) are currently in dispute (1---15). Some evolutionists believe (i) that a single rooted and dichotomously branching representation of the relationships between all life forms is appropriate (at all levels above species), because it best represents their history; (ii) that we can with available data and methods reconstruct this tree quite accurately; and (iii) that we have in fact done so, at least for the major groups of organisms. Other evolutionists question the second and third of these beliefs, holding that data are as yet insufficiently numerous and phylogenetic models as yet insufficiently accurate to allow reconstruction of life's earliest divisions, although they do not doubt that some rooted and dichotomously branching tree can in principle represent the history of all life. Still other evolutionists, ourselves included, question even this most fundamental belief, that there is a single true tree. All sides express confidence in their positions, and the debate often seems to be at an impasse (see for instance refs. 9---12).

Paul Nelson -

I notice you ignored my earlier post.

Let's review the overall situation. The extreme similarity of bacterial and human ribosomes was presented as a drop in the ocean of evidence in favor of the common descent of modern life, a single drop in itself sufficient to demonstrate the vacuity of ID.

You aren't arguing "for ID" in this thread. You're merely arguing against this single tiny drop of evidence for evolution. Let's not forget that a massive ocean of equally good evidence gave forth this drop, nor that, even if bacterial ribosomes did not share ancestry with eukaryotic ribososmes, that alone would hardly justify the adoption of ID, or the abandonment of the theory of evolution.

You wrote -

"Answer: the [biochemical] differences would be too great to allow preservation of function during the transformation of structure from a common ancestor. That is, the differences would violate what Francis Crick and Leslie Orgel called the Principle of Continuity: the only absolutely necessary condition for any evolutionary transformation is that essential function not be lost. No postulated evolutionary transformation can violate the Principle of Continuity."

I'm not sure why Crick and Orgel said this. It's often true, but not always. Gene duplications, followed by the evolution of a different function for one of the copies, have been advanced as an example. Many other examples abound (bats and birds use their "arms" to fly, seals use them to swim, humans don't use them for locomotion at all except very early in life and under unusual circumstances, to demonstrate a facile one). However, my main argument is hardly with Crick, and there are cases where what he said does apply.

Moving on...

"Observed (real) differences between eukaryotic mitochondrial ribosomes and bacterial ribosomes do not count, for Art and others, as evidence sufficient to trigger the Principle of Continuity. That means they must know the Principle of Continuity has been satisfied: the changes required to transform the common ancestral ribosome into the different systems we see today are known to be biologically possible."

Correct.

"What's the observational (or experimental) evidence that ribosomes could jettison a structural unit such as 5S rRNA, without loss of function?"

Obviously, the fact that both bacterial and eukaryotic ribosomes do function can easily be observed.

I guess that settles that.

And yes questions may be asked of some difficulties, or putative difficulties, however denying the relatedness of German and English is so outrageous as not to be a starting point to any serious discussion.

yet at what point would anybody be justified in denying that observable processes could, in principle, be responsible?

If similarities are evidence of common ancestry, then dissimilarities are evidence of --- what?

Well, now, hold it. If you want to just pick one item and that's supposed to prove relationship, did you know that human Cytochrom [sic] C is closest to a sunflower? So really the sunflowers are our closest relative folks. It depends what you want to compare. If you want to compare the eyes, we are closest to an octopus. Not a chimpanzee. Pick something. What do you want to compare? Human blood specific gravity is closest to a rabbit or a pig. Human milk is closest to a donkey. It depends on what you want to compare. Pick something. If there were not some similarities between us and other animals we could only eat each other. So God designed all animals from the code so we could eat other plants and animals and digest them. Not proof for evolution. It's proof of a common Designer!

Nick wrote: "Well, after holding up these signs for a while, the men on stage noticed and decided to answer one of them. They chose the last one, regarding ribosomes. Immediately, the only person on stage with any knowledge of biology, Michael Behe, took up the question.

His answer was that ID theory does not allow for explanations regarding interspecies commonalities such as those implied in the question."

Nick, given that Behe accepts common descent, I find it difficult to believe that he gave this answer. As much as I respect your intellect and general honesty, I can't help but suspect that you've left out part of Behe's answer. Perhaps not on purpose. All of us are guilty of not remembering completely, from time to time.

Hypothesis 1: All living organisms today share common ancestry. [...] If you feel that Woese or Doolittle specifically reject Hypothesis 1, present clear evidence for it.

Extant life on Earth is descended not from one, but from three distinctly different cell types.

Thus, there is no more reason to imagine only a single first kind of cell as the progenitor of all contemporary life than there is to imagine only Adam and Eve as progenitors of the human species.

"What's the observational (or experimental) evidence that ribosomes could jettison a structural unit such as 5S rRNA, without loss of function?" Obviously, the fact that both bacterial and eukaryotic ribosomes do function can easily be observed.

I asked if any experimental evidence existed, showing that ribosomal function would not be destroyed if a structural RNA were removed.

Paul Nelson writes:
"Douglas and DMA,

If similarities are evidence of common ancestry, then dissimilarities are evidence of --- what?"

Subsequent evolution, including selection and drift.

Sheesh.

"Put another way, what molecular characters would show that eukaryotic mitochondrial ribosomes and bacterial ribosomes arose independently of each other? One cannot say that similarities count as evidence for common ancestry, unless one knows what would count as evidence against common ancestry."

Can you arrange the patterns of similarity in a nested heirarchy? If not, then that is evidence against common ancestry.

Now, Paul, tell us again, how you falsify ID?

Hypothesis 1: All living organisms today share common ancestry. Hypothesis 2: All modern life arose from a single origin, as opposed to there being multiple origins, the descendants from which combined at some point early in life's history. Hypothesis 3: The Tree of life is dichotomous, as opposed to there being any lateral transfer or re-joining of separate lineages. Hypothesis 1 is not the same as Hypotheses 2 and 3. Don't pretend that it is. I would not be surprised if Woese or Doolittle reject Hypotheses 2 and/or 3 for the events very early in the history of life. I don't know of any serious scientist who rejects Hypothesis 1. If you feel that Woese or Doolittle specifically reject Hypothesis 1, present clear evidence for it.

Both Woese and Doolittle have consistently argued over the past decade that extant life on Earth descends from more than one cell (organism). On their view, there never was a universal common ancestor, meaning an organism to which all extant life traces its ancestry. For Woese, the original cellular ancestors of the three domains --- Eukarya, Archaea, Bacteria --- arose independently: their cellular architectures represent a polyphyletic geometry. Woese writes:

Extant life on Earth is descended not from one, but from three distinctly different cell types.

Carl R. Woese, "On the evolution of cells," PNAS 99 (June 25, 2002):8742-8747. For his part, Doolittle argues that the base of the tree of life represents a mangrove (multiple independent roots terminating in the prebiotic milieu), and, like a mangrove, no single root draws all the others together, as would be necessary under a strictly monophyletic geometry. Under the heading, "Is a single universal ancestral cell or species really necessary?" Doolittle argues

Thus, there is no more reason to imagine only a single first kind of cell as the progenitor of all contemporary life than there is to imagine only Adam and Eve as progenitors of the human species.

W.F. Doolittle, "The nature of the universal ancestor and the evolution of the proteome," Current Opinion in Structural Biology 10 (2000):355-358.

Paul,

How do Woese and Doolittle explain the fact that all three domains use exactly the same genetic code? How do they explain the nested hierarchy of ribosomal gene sequences? How do they explain all of the other shared commonalities if there were three independent origins?

Now drastically different genetic codes or complete lack of ribosomes in one domain, that would be evidence of independent origins.

Earlier I posted a link to the pdf, but with other links. Should have known that would get it held up.

W.F. Doolittle and E. Bapteste, "Pattern pluralism and the Tree of Life hypothesis".

It's about microbes, lateral gene transfer, and how far back the common ancestor was. There is or was enough lateral gene transfer so that a tree is not a complete model of prokaryote relations. This hardly implies the Designer did it. Lateral transfer means more evolution; evolution works even better than we used to know. Search for the paper at Sandwalk for more discussion.

Paul Nelson -

You wrote -

"What's the OBSERVATIONAL (or experimental) evidence that ribosomes could jettison a structural unit such as 5S rRNA, without loss of function?"

Emphasis mine.

I wrote -

"Obviously, the fact that both bacterial and eukaryotic ribosomes do function can easily be observed. I guess that settles that."

My tone may be light, but the fact is, this is a painfully obvious answer to your question as posed. Although 5s rRNA is not necessarily useless, ribosomes that lack it can be observed to function. Here's a link to a basic discussion.
http://users.rcn.com/jkimball.ma.ultranet/BiologyPages/R/Ribosomes.html

I also wrote about the massive amount of other evidence for evolution; you chose to ignore that.

But you replied...

"You've assumed that different ribosomes share a common ancestor, and thus that any differences, such as numbers and types of structural rRNAs, evolved without disrupting function. That was however the point at issue. I asked if any experimental evidence existed, showing that ribosomal function would not be destroyed if a structural RNA were removed."

Emphasis mine.

First of all, I never made an "assumption" about ribosomes in my life; it is the evidence that shows that ribosomes share a common ancestor.

Second of all, now you want an "experiment". Of course, such an experiment is technically very possible. We can't directly test that the earth goes around the sun by experiment (apologies if you perceive the heliocentric solar system as heresy); we can do indirect experiments only for that. We rely mainly on observation. But we could probably show, experimentally, what we already know observationally - that even in the abscence of a subunit, ribosomes will assemble and retain some function.

Probably such experiments have been done, not for the idiotic reason of responding to obsessive creationists, but to learn more about ribosomal physiology. In fact, there is a literature on the function of the 5s subunit.

But you don't really want an experiment (you'd look for one yourself if you did), you just want to keep denying, largely by pretending that you said something other than what you originally said, that your point has been refuted.

You've been knocked out twice now. If you get up and begin swinging your fists again, you'll be the only one in the ring, in an empty arena.

Well, I guess I was a bit more harsh than I intended during that last comment.

I certainly don't feel guilt. Paul Nelson was being very slippery. First arguing against the similarities between the various types of ribosomes, while ignoring all the other evidence for evolution, and not providing the slightest insight into how ID explains ribosomes. Then changing his question when he got a very simple answer.

Still, I'm trying these days to be less curmodgeonly.

Harold,

I don't think you were being all that harsh. After all Nelson has definately been playing us.

Nelson claimed that you can't use similarity as evidence for common ancestry if you don't know what would count as evidence against common ancestry.

I replied that since all known organisms did share a common ancestor similarity is indeed evidence of common ancestry and I gave a list of criteria that could be used to infer that organisms did not share common ancestors.

Nelson replies that not everyone believes that all known organisms shared a common ancestor and cites references. Huh, I guess he knew all along what would constitute evidence against common ancestry.

I replied that this hypothesis does not account for the similarities between all known life forms. After all, none of the criteria I cited were fulfilled.

Nelson runs away without answering.

It's always preferable to be civil. I do appreciate you guys putting up with me. But this guy just seems to want to play games.

As fascinating and often amusing as this discussion has been, I'd like to drag things back to the OT for a moment. For those who haven't followed up Nick's link to the SMU Daily Campus in detail, there's been ID content on the opinion page for every day in the past week. The reader comment sections have been very lively (if occasionally buggy on a technical level). IDists of the most ignorant and pugnacious sort are all over it. Friday saw an op-ed piece by a Spanish lecturer at the university. Choice excerpts:

"I, for one, am weary of this arrogant stranglehold on knowledge, and science so-called, as if there were a single scientist or philosopher anywhere in the world who was there when it all happened (evolution, creation, the Big Bang) and saw God not do it!"

"Scientific materialists have been force-feeding me their one-sided perspective on reality for way too long."

"If there is a Creator, then what we see around us is at best the debris of the creation event, whatever form it may have taken. Would you put much confidence in a Theory of French Cuisine based only on an analysis of the egg and flour spillage on the countertop and floor?"

Really, I'm not making those up. Anyway, there's plenty of pushback from sharper minds, but one or two people from around these parts would be welcome. Clearly there are a lot of eyes watching those pages, many of them probably people who don't give much thought to this subject otherwise (unlike most people who come here, I would imagine). At the very least, it's entertaining to read.

Paul Nelson wrote:
"If similarities are evidence of common ancestry, then dissimilarities are evidence of --- what?"

This is a creationist straw man. The evidence for common ancestry is not simply similarity. The evidence is the pattern and extent of similarities, which necessarily involves looking at differences too.

"Put another way, what molecular characters would show that eukaryotic mitochondrial ribosomes and bacterial ribosomes arose independently of each other?"

Their failure to fit into a nested hierarchy, of course.

"One cannot say that similarities count as evidence for common ancestry, unless one knows what would count as evidence against common ancestry."

We don't simply say the former, and we clearly know the latter.

You are a very dishonest man.

Interesting announcement from UCI.

BACK TO DARWIN
Francisco Ayala, the UC Irvine biologist who won the National Medal of Science for groundbreaking work in evolutionary genetics and the origins of disease, will give a pair of free public lectures today and Thursday about Darwinism and intelligent design.

His first appearance comes at 7 p.m. today, when Ayala, a former Franciscan priest, gives a talk titled "Evolution and Religion: Concert, Not Conflict." The lecture will be held in Schneiderman Hall, on Ring Road, next to McGaugh Hall.

On Thursday, Ayala will visit Chapman University in Orange to discuss "Darwin and Intelligent Design." The talk gets started at 4 p.m. in Beckman Hall. He will accept questions from the audience after both lectures.

childish word-game playing

yep that's exactly how i would put paul nelsons short answer

however,i would like to see his long answer (and the subsequent refutations)

btw,does anyone know anything more about "hatena" and that sort of "precursor" secondary endosymbiosis that some japanese researchers found last year ?

there was a short article in Science about it